Canberra's rowers and sailing enthusiasts fear lower levels in Lake Burley Griffin will prevent them from using the popular waterway for the next year.

Authorities have reduced the water level in the lake by 0.5 metres to allow workmen to replace 120 corroded bolts on the gates of Scrivener Dam.

The repair work is expected to cost up to $20 million and will take up to 18 months to complete.

But groups which use the lake for recreation and sport say the lower level is making it harder to launch their rowing and sail boats, and to navigate the lake safely.

ACT Rowing president David Bagnall says it is creating significant health and safety problems for school rowing programs.

"Some of the schools are talking of closing down," he said.

"It's getting near the end of term, but they are really worried about their rowing programs and are looking for some sort of solution that will enable them to continue into the future."

The National Capital Authority's (NCA) Gary Rake says he is working on a solution and has appealed for patience.

"Once people are out on the lake we expect the majority of activities to be able to continue," Mr Rake said.

"But we'd ask all users to take a little bit of extra care particularly the first time they navigate their frequent part of the waterway because some of the submerged items, logs or rocks, will now be half a metre closer to the surface."

The NCA is also investigating the large numbers of dead fish found on the shores of the lake in the past fortnight.

On average, five dead carp are found around the lake each day. But that number has increased dramatically, with 60 dead carp found one day last week.

The NCA insists the dead fish are not linked to the lowering of the lake's level.

Mr Rake says the native fish have not been affected and no one knows what is killing the carp.

"All of the water quality testing that we do is based around protecting human health and those results have been very normal," he said.

"In fact the lake has been pretty clear until just the last week. We're starting to see a little algae and bacterial level elevation but nothing to explain the death of the carp."